| Cluster | Node ID in cluster | Pathways | Pathway name and function | Mechanism |
| 1 | VEGFD, VEGFB, VEGFA, PDGFB, PDGFA, CUL7, CUL5, CUL4B, CUL4A, CUL3, CUL2, CUL1, CACUL1 | Endocytosis Bacterial invasion of epithelial cells EGFR receptor signaling Golgi-associated vesicle biogenesis Signal transduction Clathrin-derived vesicle budding | Mycobacterium can exploit the formation of new blood vessels to facilitate its dissemination via VEGF-related signaling pathways [36]. Upregulation of PEGF secreted by alveolar macrophages upon mycobacterium infection and in company with the EGFR signaling pathway manipulates host lipid metabolism [37]. Cullins (CUL) provide a scaffold for ubiquitin ligases (E3) involved in protein catabolism [38]. |
| 2 | TGFBR1, TCF7, TCF4, PRKG1, MAN1A2, GNAI1, EDEM1, CTNNB1 | TGF-β receptor signaling pathways Adherents junction Focal adhesion Regulation of lipid metabolism Fatty acid, triacylglycerol, and ketone body metabolism | Regulation of the immune system Mycobacterium dissemination Metabolism and catabolism |
| 3 | SOS1, PANK3, IQGAP1, PRKCA, INPP4B, PIKFYVE, MAN2A1 | N-Glycan biosynthesis Proteasome degradation Asparagine N-linked glycosylation T-Cell receptor and costimulatory signaling ErbB signaling pathway Downstream signaling of activated FGFRs VEGFA-VEGFR2 pathway | Metabolism and catabolism Immune system regulation New vessel formation |
| 4 | UBE2W, SMURF2, RYR2, PTEN, PLCZ1, MAN1A1, GRM1, GNAQ | Ubiquitination & proteasome degradation Calcium signaling pathway Class I MHC-mediated antigen processing & presentation Gap junction Inositol phosphate metabolism Insulin secretion Phosphatidylinositol signaling system Phospholipid metabolism | Adaptive immune system Antigen processing: Metabolism and catabolism |
| 5 | VEGFC, ST6GAL1, PRKCB, PLN, PIK3CD, PDGFD, ORAI3, OCRL, MAN2C1, MAN2B1, MAN2A2, LEF1, HERC3, EDEM2 | Calcium signaling pathway Focal adhesion Asparagine N-linked glycosylation Beta-catenin-independent WNT signaling Downstream signaling events of B cell receptor (BCR) IL-3 signaling pathway N-glycan antennae elongation in the medial/trans-Golg Phosphatidylinositol signaling system PI metabolism Rap1 signaling pathway Ras signaling pathway Signaling by receptor tyrosine kinases | Metabolism and catabolism Modulation of signaling pathways Cytokines modulation |
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